A damning report on St Patrick's Institution in Dublin has found a culture that led to the human rights of some children and young adults being either ignored or violated.
The Inspector of Prisons, Judge Michael Reilly, also raised concerns about prison healthcare and education, as well as the use of control and restraint techniques.
Minister for Justice Alan Shatter described the findings as shocking and said the Government would not tolerate the type of abuse outlined in the report.
The report found many officers working in St Patrick's have not been adequately trained to deal with young people.
It says many children and young adults who are on "protection" are locked up for 23 hours a day.
Judge Reilly said this "offends against all that should be expected of a civilised society in the 21st century".
Some children and young adults were dealt with under the disciplinary procedure, which resulted in the prohibition of contact with family by way of visit.
This is contrary to European prison rules.
The report found prisoners are stripped of their clothing and required to wear an under garment and a poncho style over garment when placed in safety observation cells for management purposes.
Judge Reilly said prisoners should only be placed in these cells for medical purposes.
To force prisoners to undress in this manner was "degrading and a form of punishment, intimidation and abuse".
In one instance, the report says bedclothes had not been changed after the previous occupant after a child was placed in a cell in the children's wing.
"The bed clothes were dirty, the toilet was blocked and he had no running water," the report says.
This was brought to the attention of management but the bed clothes were not changed for four further days.
Young people have no 'chance to better themselves'
On many of his visits, the inspector found many of the cells were dirty, needed painting and did not have adequate furniture.
Many other areas were dirty, unhygienic and had broken equipment.
Judge Reilly says it is an indictment of St Patrick’s that many prisoners leave without having had a chance to better themselves.
He also states that while illegal drugs and contraband are a problem in all prisons, it appears the situation is worst in St Patrick's with most being thrown over the walls of the institution.
The psychology service is overstretched and there is anecdotal evidence that medical referrals to outpatient departments of hospitals were often delayed for hours or days.
He says a review he commissioned found the delays in referrals were unacceptable and carry potential serious risks.
The prison doctor's instructions are carried out appropriately, he added.
The inspector said that in 2010 he reported that the safety observation cell was being used in the majority of cases for management purposes and this was not best practice.
He says he is sorry to report that his advice was ignored.
Judge Reilly also found that the detention of children in St Patrick's should end as a matter of urgency and the current timeline of May 2014 for ending their detention should be revisited.
He says the prisoners in St Patrick's do not have the capacity to organise structured activity for themselves, and even if they did, he points to the lack of such aids as footballs.
The vast majority of officers show respect to and understanding of the prisoners in their care and they act in a professional manner when at times, the report says, circumstances can be very challenging.
He also says a youth sex offenders' programme has been developed in the prison and is working successfully.
He notes that in April of this year the Minister for Children and Youth Affairs Frances Fitzgerald said she had secured funding to end the detention of children in St Patrick's.
From 1 May, all newly-remanded children or sentenced 16-year-olds will be detained in the children's detention facilities at Obserstown.
Within two years, it is the intention that all of those under 18 years will be sent to dedicated child specific facilities on the Oberstown campus.
Responding to the report, Minister Shatter said that neither he nor the Government would tolerate "this type of abuse".
"I have instructed the Director General of the Irish Prison Service to ensure that everything possible is done to address these issues within the timeframes set by the Inspector if not before then."
He said a new Governor has been appointed along with two new Assistant Governors.
A further senior management position is to be filled by mid-October.
Irish Prison Service Director General Michael Donnellan said the report detailed an inflexible, rigid culture with an over-emphasis on control and security.
He said steps have been taken in recent months to address the issues raised in the report.
The Irish Penal Reform Trust said the report calls into question the viability of continuing to operate St Patrick's Institution.